Caked in dust and bristling with weaponry, the Tuareg rebels smiled at Neil Whitehead and Diane English. “It’s O.K., we’re here for your protection,” one of the veiled warriors grinned at the nervous couple. Caught up in the middle of a war after Tuareg separatists advanced hundreds of miles in a matter of hours, the hotel owners had tried twice already to leave their adopted home of Timbuktu, Mali. At first, retreating army columns blocked their way. Then, when the road eventually cleared, English and Whitehead ran straight into a firefight. “There were guns going off all around us and tracer going past the cab windows, and we thought, ‘This isn’t good,'” English says, with a flash of understatement.

Yet the real threat came not from the National Movement for the Liberation of Azawad (known by its French acronym, MNLA) — the 1,000 or so secular Tuareg separatists who on Friday declared independence — but Islamist militants and al-Qaeda emirs busy hijacking its campaign. As Timbuktu fell, French diplomats brokered a deal to spirit English, Whitehead, their “leggy Saharan desert dog” Lily and a French citizen also trapped in the fabled city to safety. Wearing turbans to disguise themselves and taking only those belongings they could carry, the fugitives piled into Tuareg pickups — and then camped and drove, camped and drove, “belting through the desert hell for leather,” English says. The rebels “really were fantastic … From the time we put ourselves in their hands … although I knew we weren’t yet safe, I wasn’t really concerned.”

Two days and 850 miles (1,370 km) of hard driving later, they arrived in Mauritania’s seaside capital of Nouakchott, dusty, tired, rattled — and relieved. “Having a shower and a change of clothes was an absolute luxury,” says English. Yet happy ending aside, the flight through the desert underscores one of the most unsettling aspects of Mali’s Tuareg revolt: how al-Qaeda’s regional franchise has been able to exploit the instability in northern Mali much more, and much faster, than almost anyone anticipated. The first worrying signs emerged Monday with reports that Mokhtar Belmokhtar, the Algerian-born leader of al-Qaeda in the Islamic Maghreb (AQIM), had been spotted in Timbuktu, alongside two other prominent AQIM commanders, Abou Zeid and Yahya Abou al-Hammam. “It’s extremely difficult to evaluate the claims and reports coming out of Timbuktu,” says to Andrew Lebovich, an analyst with the Navanti Group who focuses on Sahelian issues. But “multiple sources cite eyewitnesses who say they saw one or several AQIM leaders.” As civilians fleeing Timbuktu impart fresh accounts of what is happening in the desert city, the number of claims are steadily growing.

What is more certain is that at the same time as the purported sightings, a Salafi group called Ansar Eddine drove the mainstream Tuareg rebels out of Timbuktu with a show of force — and promptly set about briefing those civilians who have not fled on the dictates of Shari‘a, which they say they plan to impose. “Our war is a holy war,” Omar Hamaha, one of the group’s commanders said to inhabitants this week. “It’s a legal war in the name of Islam.” As for 120 prisoners Hamaha claimed the militants had taken, “We have tied them up and taken their weapons. We beat them well, and it’s likely we will slit their throats.” In another northern Malian town called Gao, meanwhile, fighters from the Movement for Unity and Jihad in West Africa, which is linked to al-Qaeda, have taken a visible role in the fighting.

The big question is why the more numerous rebels of the MNLA have allowed smaller groups of religious militants to hijack their explicitly secular campaign. According to a Tuareg source close to the MNLA, the conventional wisdom is that though “the MNLA is stronger and better equipped than Ansar Eddine and AQIM,” it cannot conduct “two wars at once” and must concentrate on its struggle against the Malian state before purging the Islamists in its midst. With the Islamists growing bolder by the day, it’s a dangerous decision.

Citing international law and precedent and echoing the language of the U.S. constitution, the MNLA declared independence on Friday, saying, “We, the people of Azawad … proclaim irrevocably the independent state of Azawad from this day forth.” The U.S., France, Algeria, the African Union and the E.U. have all dismissed the move, with the African Union calling it “null and of no value whatsoever” and a French minister saying the unilateral declaration “which is not recognized by African states [had no] meaning for us.” A U.S. diplomat in Bamako said the priority in Mali remained “the regional threat posed by AQIM, a transborder criminal-terrorist organization,” and that the country had to move toward a “constitutionally appropriate” way of tackling this.

Amnesty International, meanwhile, warned that Mali was on the brink of a “major humanitarian disaster” in the wake of the rebellion, as looting, kidnappings and rapes go unchecked. In the town of Gao, sacked a week ago, one inhabitant told TIME of a descent into chaos as Islamist militants trashed an evangelical church near his house, a nightclub and the Algerian consulate. “I saw someone [from al-Qaeda] driving the consul’s car,” he said. “They have big beards and their flag … their black flag with white writing.” In Gao, as in every town the rebels have taken, food and medicine are running out. “We can’t drink [river water] all the time,” the man said. “People are saying they’re killing us without [firing their guns]. I don’t think the electricity and water will last for long. People are getting hungry and hungrier.”